I tried running HOMER script annotateInteractions.pl for custom genome that I loaded using loadGenome.pl script for cotton. The annotation file generated does not have detailed annotations, gene name, gene alias although all these information were present in the gtf file.

I also tried updateUCSCGenomeAnnotations.pl for cotton genome bit the necessary files are not present on the UCSC server due to which it throws error. How can I get the detailed annotations along with the gene names in the annotation file being generated by annotateInteractions.pl